4OCD | pdb_00004ocd

In and Out the minor groove: Interaction of an AT rich-DNA with the CD27 drug

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	288.15	0.25 mM DNA duplex, 0.75 mM CD27, 40 mM sodium cacodylate buffer pH 6.5, 8 mM MnCl2 , 0.5 mM spermine and 5% MPD equilibrated against a 30% MPD reservoir, VAPOR DIFFUSION, HANGING DROP, temperature 288.15 K

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 78.013	α = 90
b = 78.013	β = 90
c = 91.552	γ = 120

Symmetry
Space Group	P 61 2 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	PIXEL	DECTRIS PILATUS 6M		2013-07-19	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALBA BEAMLINE XALOC	0.97949	ALBA	XALOC

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym I (Observed)	Net I Over Average Sigma (I)	Redundancy	Number Reflections (All)	Number Reflections (Observed)	Observed Criterion Sigma (F)	Observed Criterion Sigma (I)	B (Isotropic) From Wilson Plot
1	2.1	39	99.8	0.036	0.036	30.2	11.4		10091	2	2	59.64

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.1	2.21	99.84		0.58	3	6.85	1433

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	2.1	39	9432	480	97.91	0.23682	0.23614	0.24	0.25103	0.26	RANDOM	60.32

Temperature Factor Modeling
Anisotropic B[1][1]	Anisotropic B[1][2]	Anisotropic B[1][3]	Anisotropic B[2][2]	Anisotropic B[2][3]	Anisotropic B[3][3]
-3.21	-1.61		-3.21		10.42

RMS Deviations
Key	Refinement Restraint Deviation
r_long_range_B_other	13.424
r_long_range_B_refined	13.348
r_scangle_other	10.895
r_mcbond_it	9.295
r_scbond_it	7.309
r_scbond_other	7.303
r_angle_other_deg	7.222
r_angle_refined_deg	1.653
r_chiral_restr	0.069
r_bond_refined_d	0.024
r_bond_other_d	0.008
r_gen_planes_refined	0.008
r_gen_planes_other	0.006
r_dihedral_angle_1_deg
r_dihedral_angle_2_deg
r_dihedral_angle_3_deg
r_dihedral_angle_4_deg
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_it
r_mcangle_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms
Nucleic Acid Atoms	483
Solvent Atoms	64
Heterogen Atoms	75

Software

Software
Software Name	Purpose
PHASER	phasing
REFMAC	refinement
XDS	data reduction
SCALA	data scaling